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annotate lofreq_viterbi.xml @ 0:33a416e1659e draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
author iuc
date Tue, 17 Dec 2019 17:25:37 -0500
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children ecd80c7c3886
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33a416e1659e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
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1 <tool id="lofreq_viterbi" name="Realign reads" version="@WRAPPER_VERSION@0" python_template_version="3.5">
33a416e1659e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
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2 <description>with LoFreq viterbi</description>
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
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6 <expand macro="requirements">
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7 <requirement type="package" version="1.9">samtools</requirement>
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8 </expand>
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9 <command detect_errors="exit_code"><![CDATA[
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10 @PREPARE_REF@
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11 lofreq viterbi --ref '$reference_fasta_fn' --out - $keepflags --defqual $defqual '$reads' | samtools sort - -O BAM -o '$realigned'
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12 ]]></command>
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13 <inputs>
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14 <param name="reads" type="data" format="bam" label="Reads to realign" />
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15 <expand macro="reference_interface" />
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16 <param argument="--keepflags" type="boolean" truevalue="--keepflags" label="Don't delete flags MC, MD, NM, and A" help="These flags are all prone to changing during realignment" />
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17 <param argument="--defqual" type="integer" value="-1" label="Quality to assume for all bases with BQ2" />
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18 </inputs>
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19 <outputs>
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20 <data name="realigned" format="bam" label="${tool.name} on ${on_string}: Realigned reads" />
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21 </outputs>
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22 <tests>
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23 <test>
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24 <param name="reads" ftype="bam" value="lofreq-in1.bam" />
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25 <param name="ref_selector" value="history" />
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26 <param name="ref" ftype="fasta" value="pBR322.fa" />
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27 <output name="realigned" file="viterbi-out1.bam" />
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28 </test>
33a416e1659e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
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29 <test>
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30 <param name="reads" ftype="bam" value="lofreq-in1.bam" />
33a416e1659e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
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31 <param name="ref_selector" value="history" />
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32 <param name="keepflags" value="true" />
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33 <param name="ref" ftype="fasta" value="pBR322.fa" />
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34 <output name="realigned" file="viterbi-out2.bam" />
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35 </test>
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36 </tests>
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37 <help><![CDATA[
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38 Usage: lofreq viterbi [options] in.bam
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39
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40 Options:
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41 -f | --ref FILE Indexed reference fasta file [null]
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42 -k | --keepflags Don't delete flags MC, MD, NM and A, which are all prone to change during realignment.
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43 -q | --defqual INT Assume INT as quality for all bases with BQ2. Default (=-1) is to use median quality of bases in read.
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44 -o | --out FILE Output BAM file [- = stdout = default]
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45 --verbose Be verbose
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46
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47 NOTE: Output BAM file will (likely) be unsorted (use samtools sort, e.g. lofreq viterbi ... | samtools sort -')
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48
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49 ]]></help>
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50 <expand macro="citations" />
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51 </tool>